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The animated series used basically the same formula as the HBO original, including the same theme song. Many episodes consisted of two 15-minute stories; however, a few presented a single full 30-minute plot. The animated version carried on the tradition of original songs, with at least one tune per episode (including a few recycled from the puppet version, such as "Let Me Be Your Song"). In its original run, the animated episodes were book-ended by footage of the original puppet version of Uncle Traveling Matt, introducing the show from Doc's workshop. The animated version of Fraggle Rock ended after only one season (13 episodes).

A major running gag in the series had a butterfly collector upstaging all of the characters. This gag is broken when the collector gets captured by an animated version of Muppet monster Big V.